Amber Archive Dec 2019: by date

Sunday, 1 December 2019
- [AMBER] On deprotonated Tyr David Sáez
- [AMBER] sequence command ankita mehta
- [AMBER] Charge distribution in molecule Aashish Bhatt
- Re: [AMBER] Charge distribution in molecule Horn, Anselm
Monday, 2 December 2019
- Re: [AMBER] sequence command ankita mehta
- Re: [AMBER] Charge distribution in molecule Bill Ross
- [AMBER] cpptraj RMS calculations appear to be incorrect Bellesis, Andrew G
- Re: [AMBER] cpptraj RMS calculations appear to be incorrect Carlos Simmerling
- [AMBER] Chemical education for MD articles Lod King
- Re: [AMBER] Chemical education for MD articles Joanna Michelle E. Chua
Tuesday, 3 December 2019
- [AMBER] 34th Molecular Modelling Workshop (MMWS) February 17-19, 2020 in Erlangen, Germany Dr. Anselm Horn
- [AMBER] TI support for CHARMM FF Jose Christian Flores Canales
- Re: [AMBER] Chemical education for MD articles Daniel Roe
- Re: [AMBER] Chemical education for MD articles Joanna Michelle E. Chua
- Re: [AMBER] Obtaining excess molar volumes using Molecular Dynamics David Case
- Re: [AMBER] cpptraj RMS calculations appear to be incorrect Bellesis, Andrew G
- Re: [AMBER] help on this error Debarati DasGupta
Wednesday, 4 December 2019
- [AMBER] Announcement: 34th Molecular Modelling Workshop (MMWS) Feb 17-19, 2020 in Erlangen, Germany Dr. Anselm Horn
- [AMBER] Table 21.1 in Thermodynamic Integration section of amber18 manual Debarati DasGupta
- [AMBER] Sequential equilibration versus parallel runs in TI Debarati DasGupta
- Re: [AMBER] Sequential equilibration versus parallel runs in TI Debarati DasGupta
- Re: [AMBER] TI on gpus Debarati DasGupta
- [AMBER] MMPBSA mmpbsa_py_energy failed with prmtop Qing Lv
- Re: [AMBER] MMPBSA mmpbsa_py_energy failed with prmtop Qing Lv
Thursday, 5 December 2019
- Re: [AMBER] Charge distribution in molecule Aashish Bhatt
- Re: [AMBER] Sequential equilibration versus parallel runs in TI David A Case
- Re: [AMBER] TI on gpus David A Case
- [AMBER] Fixed Minimization emanuele falbo
- [AMBER] TI calculation steps Debarati DasGupta
- Re: [AMBER] TI calculation steps Song, Lin
- Re: [AMBER] TI calculation steps Debarati DasGupta
- Re: [AMBER] TI calculation steps Song, Lin
- Re: [AMBER] TI calculation steps Debarati DasGupta
- [AMBER] Equilibriation input file for TI Debarati DasGupta
- [AMBER] TI calculations linear scaling of atoms! Debarati DasGupta
- [AMBER] fxyz and outxyz Baker, Joseph
- [AMBER] Warning: 2 or more molecules (3 and 4) share residue numbers (1003). David Sáez
- Re: [AMBER] Warning: 2 or more molecules (3 and 4) share residue numbers (1003). Bill Ross
Friday, 6 December 2019
- [AMBER] Conference Announcement: Molecular Modeling Workshop, Feb 17-19, 2020 in Erlangen, Germany Dr. Anselm Horn
- Re: [AMBER] help on this error Josh Berryman
- [AMBER] How can I get solute-solute energy information? Zhonghua Xia
- Re: [AMBER] help on this error Debarati DasGupta
- Re: [AMBER] Fixed Minimization David A Case
- Re: [AMBER] Equilibriation input file for TI David A Case
- Re: [AMBER] Warning: 2 or more molecules (3 and 4) share residue numbers (1003). David A Case
- [AMBER] How can I get solute-solute energy information? Zhonghua Xia
- Re: [AMBER] Fixed Minimization emanuele falbo
- [AMBER] Segmentation Fault when running constant pH Replica Exchange on GPUs Hofer, Florian
- Re: [AMBER] Equilibriation input file for TI Debarati DasGupta
- [AMBER] Problems adding molecule on Metal-Water system Lucas Bandeira
- Re: [AMBER] help on this error Debarati DasGupta
Saturday, 7 December 2019
- Re: [AMBER] help on this error David Case
- Re: [AMBER] Problems adding molecule on Metal-Water system David Case
- [AMBER] problem of compiling Albert
Sunday, 8 December 2019
- Re: [AMBER] problem of compiling Charo del Genio
- [AMBER] Timestep (dt) in TI calculations Debarati DasGupta
- Re: [AMBER] Problems adding molecule on Metal-Water system Lucas Bandeira
- Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom Bill Ross
Monday, 9 December 2019
- Re: [AMBER] problem of compiling Gerald Monard
- Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom David Case
- Re: [AMBER] Problems adding molecule on Metal-Water system David Case
Tuesday, 10 December 2019
- [AMBER] error MYRIAN TORRES RICO
- Re: [AMBER] error David A Case
- Re: [AMBER] error MYRIAN TORRES RICO
- Re: [AMBER] error Daniel Roe
- [AMBER] Molecular dynamics of tripeptide like organic molecule Debasish Mandal
- Re: [AMBER] Molecular dynamics of tripeptide like organic molecule Petro
Wednesday, 11 December 2019
- [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling
- Re: [AMBER] error MYRIAN TORRES RICO
- [AMBER] Found an invalid periodicity in the prmtop file : MMPBSA venkat
- Re: [AMBER] error David A Case
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná
- Re: [AMBER] error James Kress
- [AMBER] GPU installation error Sruthi Sudhakar
- Re: [AMBER] GPU installation error David A Case
- Re: [AMBER] Found an invalid periodicity in the prmtop file : MMPBSA David A Case
- Re: [AMBER] error Carlos Simmerling
- Re: [AMBER] error Bill Ross
- [AMBER] Fwd: problem of compiling Albert
- Re: [AMBER] GPU installation error Sruthi Sudhakar
- [AMBER] Time shift. Petro
Thursday, 12 December 2019
- Re: [AMBER] Time shift. Bill Ross
- Re: [AMBER] error MYRIAN TORRES RICO
- [AMBER] User-defined high precision AMBER trajectory file formats Xin Bai
- [AMBER] Found an invalid periodicity in the prmtop file : MMPBSA venkat
- Re: [AMBER] Found an invalid periodicity in the prmtop file : MMPBSA venkat
- Re: [AMBER] Fwd: problem of compiling David A Case
- Re: [AMBER] Problems adding molecule on Metal-Water system Lucas Bandeira
- [AMBER] Ti on pmemd.CUDA Hosein Geraili Daronkola
- Re: [AMBER] Ti on pmemd.CUDA Carlos Simmerling
- [AMBER] Flexible protein! Debarati DasGupta
- Re: [AMBER] Fwd: problem of compiling Gerald Monard
- [AMBER] GaMD problems with different computers. Seibold, Steve Allan
- Re: [AMBER] error Bill Ross
- [AMBER] mm-gbsa with more than one receptor Neha Gandhi
- Re: [AMBER] Fwd: problem of compiling Albert
- [AMBER] mm-gbsa with more than one receptor Liao
- [AMBER] mm-gbsa with more than one receptor Liao
- [AMBER] mm-gbsa with more than one receptor Liao
- [AMBER] mm-gbsa with more than one receptor Liao
- [AMBER] MM-GBSA error Rui Chen
- [AMBER] intel compiling failed Albert
- Re: [AMBER] Fwd: problem of compiling Gerald Monard
- Re: [AMBER] Fwd: problem of compiling Albert
Friday, 13 December 2019
- Re: [AMBER] Fwd: problem of compiling Gerald Monard
- Re: [AMBER] Flexible protein! David A Case
- Re: [AMBER] GaMD problems with different computers. David A Case
- Re: [AMBER] intel compiling failed David A Case
- [AMBER] Error when running MD maya nair
- Re: [AMBER] Error when running MD David Case
- Re: [AMBER] Error when running MD Bill Ross
- Re: [AMBER] Flexible protein! Debarati DasGupta
- Re: [AMBER] MM-GBSA error Rui Chen
- [AMBER] Any way of making protein rigid in MD simulation? Liao
Saturday, 14 December 2019
- Re: [AMBER] MM-GBSA error David Case
Sunday, 15 December 2019
- Re: [AMBER] error Daniel Roe
- Re: [AMBER] User-defined high precision AMBER trajectory file formats Daniel Roe
- [AMBER] FESetup Debarati DasGupta
- [AMBER] Problems installing mpi for AMBER 18. Billiot, Eugene
- Re: [AMBER] Problems installing mpi for AMBER 18. Bill Ross
- Re: [AMBER] Problems installing mpi for AMBER 18. Billiot, Eugene
- [AMBER] Virtual box with imin = 1 or imin = 5 Jerome Eberhardt
- Re: [AMBER] Virtual box with imin = 1 or imin = 5 Bill Ross
- Re: [AMBER] FESetup Sushil Mishra
- Re: [AMBER] Any way of making protein rigid in MD simulation? Gustaf Olsson
Monday, 16 December 2019
- Re: [AMBER] FESetup Sarah Fegan - UKRI STFC
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná
- Re: [AMBER] Virtual box with imin = 1 or imin = 5 Carlos Simmerling
- [AMBER] NVT equilibriation followed by NPT in TI Debarati DasGupta
- Re: [AMBER] Any way of making protein rigid in MD simulation? Brian Radak
- Re: [AMBER] Problems installing mpi for AMBER 18. Billiot, Eugene
- Re: [AMBER] Problems installing mpi for AMBER 18. Bill Ross
- Re: [AMBER] Problems installing mpi for AMBER 18. I was trying to install mpi I was typing in Billiot, Eugene
- [AMBER] question about Tleap Rui Chen
- Re: [AMBER] Virtual box with imin = 1 or imin = 5 Jerome Eberhardt
- [AMBER] Any idea on this error and how to troubleshoot Debarati DasGupta
- Re: [AMBER] Virtual box with imin = 1 or imin = 5 David Case
- Re: [AMBER] Virtual box with imin = 1 or imin = 5 David Case
- Re: [AMBER] Any idea on this error and how to troubleshoot Cruzeiro,Vinicius Wilian D
- [AMBER] MMGBSA script file Rui Chen
- Re: [AMBER] Virtual box with imin = 1 or imin = 5 Jerome Eberhardt
- Re: [AMBER] Virtual box with imin = 1 or imin = 5 Jerome Eberhardt
- Re: [AMBER] MMGBSA script file Rui Chen
- [AMBER] nuc.nab:no such file found error Sruthi Sudhakar
- Re: [AMBER] nuc.nab:no such file found error Bill Ross
Tuesday, 17 December 2019
- Re: [AMBER] nuc.nab:no such file found error David Case
- Re: [AMBER] NVT equilibriation followed by NPT in TI David Case
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná
- Re: [AMBER] NVT equilibriation followed by NPT in TI Debarati DasGupta
- [AMBER] tip4p-d water forcefield parameters Luca Codutti
- Re: [AMBER] tip4p-d water forcefield parameters Luca Codutti
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling
- [AMBER] Problems installing Amber 18 Billiot, Eugene
- Re: [AMBER] Problems installing Amber 18 Billiot, Eugene
- [AMBER] installing Amber 18 issues Billiot, Eugene
- Re: [AMBER] installing Amber 18 issues Joanna Michelle E. Chua
- Re: [AMBER] installing Amber 18 issues Joanna Michelle E. Chua
- Re: [AMBER] installing Amber 18 issues Billiot, Eugene
- Re: [AMBER] nuc.nab:no such file found error Sruthi Sudhakar
- [AMBER] If there is a method that can just use the soft-core potential for VDW interaction but not for electrostatic part wangjianing_mail
- Re: [AMBER] Problems installing Amber 18 Gustaf Olsson
Wednesday, 18 December 2019
- Re: [AMBER] installing Amber 18 issues David Case
- Re: [AMBER] tip4p-d water forcefield parameters David Case
- Re: [AMBER] If there is a method that can just use the soft-core potential for VDW interaction but not for electrostatic part David Case
- Re: [AMBER] Problems installing Amber 18 Billiot, Eugene
- Re: [AMBER] MM-GBSA error Rui Chen
Thursday, 19 December 2019
- [AMBER] Attaching Methoxy (OMe) Capping at C-terminal Pallab Dutta
- Re: [AMBER] Attaching Methoxy (OMe) Capping at C-terminal David Case
- Re: [AMBER] Attaching Methoxy (OMe) Capping at C-terminal Pallab Dutta
- [AMBER] cpptraj.MPI versus cpptraj Debarati DasGupta
- Re: [AMBER] cpptraj.MPI versus cpptraj David Case
- [AMBER] amber 18 installation error Saikat Pal
- Re: [AMBER] amber 18 installation error Gustaf Olsson
- [AMBER] amber update issue Saikat Pal
Friday, 20 December 2019
- Re: [AMBER] imin=5 fails to produce output Casalini Tommaso
- Re: [AMBER] cpptraj.MPI versus cpptraj Debarati DasGupta
- Re: [AMBER] cpptraj.MPI versus cpptraj Daniel Roe
- Re: [AMBER] cpptraj.MPI versus cpptraj Daniel Roe
- Re: [AMBER] cpptraj.MPI versus cpptraj Debarati DasGupta
- Re: [AMBER] cpptraj.MPI versus cpptraj Debarati DasGupta
- Re: [AMBER] amber update issue David Case
- [AMBER] Amber18 installation problem Billiot, Eugene
- Re: [AMBER] Amber18 installation problem David Case
- Re: [AMBER] Amber18 download instructions Billiot, Eugene
- Re: [AMBER] Amber18 download instructions Billiot, Eugene
- [AMBER] How to use AMBER on Supercomputer MUHAMMAD KHATTAB FATHI KHATTAB
- [AMBER] How to deal with Dummy atoms of 4-coordinated Zinc in QM/MM Qing Lv
Saturday, 21 December 2019
- Re: [AMBER] How to use AMBER on Supercomputer Liao
- Re: [AMBER] How to use AMBER on Supercomputer MUHAMMAD KHATTAB FATHI KHATTAB
- Re: [AMBER] How to use AMBER on Supercomputer Liao
- Re: [AMBER] How to use AMBER on Supercomputer MUHAMMAD KHATTAB FATHI KHATTAB
Sunday, 22 December 2019
- [AMBER] Definition of restraints to avoid ligand aggregation Giulio RASTELLI
- [AMBER] help needed for failed installation of CUDA for GPU-accelerated versions of pmemd for AMBER 18 Billiot, Eugene
Monday, 23 December 2019
- [AMBER] AMBER 18 cuda installation Saikat Pal
- [AMBER] MMGB/PBSA parameters Rui Chen
- Re: [AMBER] MMGB/PBSA parameters Carlos Simmerling
- Re: [AMBER] MMGB/PBSA parameters Rui Chen
- [AMBER] Minimization equilibration of protein+ligand prior to TI setup Debarati DasGupta
- Re: [AMBER] Minimization equilibration of protein+ligand prior to TI setup David Case
- Re: [AMBER] help needed for failed installation of CUDA for GPU-accelerated versions of pmemd for AMBER 18 David Case
- [AMBER] Amber18-bash: logFile: command not found... 辛志宏
Tuesday, 24 December 2019
- [AMBER] Error during installation ARITRA MITRA
- Re: [AMBER] Amber18-bash: logFile: command not found... David Case
- Re: [AMBER] Minimization equilibration of protein+ligand prior to TI setup Debarati DasGupta
- Re: [AMBER] Error during installation David Case
- Re: [AMBER] help needed for failed installation of CUDA for GPU-accelerated versions of pmemd for AMBER 18 Billiot, Eugene
Wednesday, 25 December 2019
- Re: [AMBER] Minimization equilibration of protein+ligand prior to TI setup Carlos Simmerling
- [AMBER] Interaction entropy program （Geng Dong）东庚
- [AMBER] Tleap naming problem Rui Chen
Thursday, 26 December 2019
- [AMBER] Which language could tleap know? mwli.mail.ustc.edu.cn
- Re: [AMBER] Tleap naming problem David Case
- Re: [AMBER] Which language could tleap know? David Case
Friday, 27 December 2019
- [AMBER] Parameters to be used for protein in implicit solvent SHAUNAK BADANI
- Re: [AMBER] Parameters to be used for protein in implicit solvent Carlos Simmerling
- Re: [AMBER] Minimization equilibration of protein+ligand prior to TI setup Debarati DasGupta
Sunday, 29 December 2019
- [AMBER] some queries Ayesha Fatima
Monday, 30 December 2019
- [AMBER] reinstalling Amber 16 + Ambertools 16 on a Mac erik zuiderweg
- [AMBER] Figured Amber 16 installation on Mac Erik Zuiderweg
- Re: [AMBER] some queries David Case
- Re: [AMBER] some queries Ayesha Fatima

Last message date: Mon Dec 30 2019 - 06:30:04 PST
Archived on: Fri Dec 20 2024 - 05:55:55 PST

Amber Archive Dec 2019 by date